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Thanks so much!

On Sat, Aug 1, 2009 at 5:33 AM, Mark Jenkinson <[log in to unmask]> wrote:
Hi Nicole,

This looks fine to me.
Sometimes I would say that we get better results for step 1
by using the skull-stripped image for T1High, but normally
it doesn't matter much as long as you stick to 6 DOF.

Everything else looks great, so should work fine.

All the best,
       Mark



On 1 Aug 2009, at 02:16, Nicole Strang wrote:

Hi,
I've primarily used afni in the past, but want to take advantage of the
great non-linear registration in fsl. Because I've already run the
first-level stats is afni, I'd like to use fsl for registration alone, if
possible. I couldn't find an answer to my the question online, so I would
really appreciate it if someone could let me know if there are any problems
with my approach. If there is a problem, alternative would be very much
appreciated.
Convert all relevant files to NIFTI
1) Register run1 epi time series (there are 4 runs but all frames are
aligned to first frame of run1) to skull on T1High (with flirt)
2) Register skull stripped T1High brain to MNI (with flirt)
3) Register skull on T1High to MNI (with fnirt)
4) Register output of glm which has been converted to percent signal change
with output of (3) as warp and output of (1) as premat.

Thanks!
Nicole




--
Nicole Strang
Child Emotion Research Lab
University of Wisconsin-Madison
1500 Highland Ave, Rm. 394
Madison, WI 53705
(608) 890-2525